Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/ceacd51a4775424c12f4d0ad6dca0d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/ceacd51a4775424c12f4d0ad6dca0d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/blacklist_breakpoint_database_2026-04-27.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/135da656991fa5953aa3a3c2ab9dd5/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-eb5d3959-7137-45a9-9f26-41f9201dcf7f/81/be38f7f47cc30e4a107d9e602cb8fb/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 2 fusion rows (breakpoint_ID in qualified set)

================================================================================
ARRIBA FILTERING SUMMARY
================================================================================

Total fusions: 92
  Pass (FILTER=PASS): 3 (3.3%)
  Fail (FILTER=FAIL): 89 (96.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 32
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(low<high): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 3 pass, 2 fail (total: 5)
  low: 0 pass, 40 fail (total: 40)
  medium: 0 pass, 47 fail (total: 47)
Arriba filter: 92 rows -> 3 PASS; wrote aih-tih-sc-242a7d-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-242a7d-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt